BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 011979
(473 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QGZ|A Chain A, Crystal Structure Of A Putative Primosome Component From
Streptococcus Pyogenes Serotype M3. Northeast Structural
Genomics Target Dr58
Length = 308
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 33/152 (21%), Positives = 57/152 (37%), Gaps = 53/152 (34%)
Query: 147 GRRSHFVSIYRWIEKY----------YGKMANGCLCVTQAMQHELAQNWGIKATVLYDQP 196
R F +I ++E+Y YG M G + AM HEL++ G+ T+L+
Sbjct: 132 SRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH--F 189
Query: 197 PEFFHPTSLEEKHELFCRLNKILHQPLGVQDCVSNGMEGQKADETIFTSLAGIDVFLKPN 256
P F + V++ +SNG ++ D N
Sbjct: 190 PSF----------------------AIDVKNAISNGSVKEEIDAV-------------KN 214
Query: 257 RPALVV------SSTSWTPDEDFGILLEAALM 282
P L++ +TSW DE ++L+ ++
Sbjct: 215 VPVLILDDIGAEQATSWVRDEVLQVILQYRML 246
>pdb|1K5M|B Chain B, Crystal Structure Of A Human Rhinovirus Type 14:human
Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus Mn-
Iii-2
Length = 277
Score = 32.0 bits (71), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 137 FGYTLLSLSLGRRSHFVSIYRWIEKYYGKMANGCLCVTQAMQHELAQNWGIKATVLYDQP 196
FG + SLGR + V + K++ +GCL V +H+LA + G +V Y
Sbjct: 92 FGQNMFFHSLGRSGYTVHVQCNATKFH----SGCLLVVVIPEHQLASHEGGNVSVKY--- 144
Query: 197 PEFFHP 202
F HP
Sbjct: 145 -TFTHP 149
>pdb|2HWB|2 Chain 2, A Comparison Of The Anti-Rhinoviral Drug Binding Pocket In
Hrv14 And Hrv1a
pdb|2HWC|2 Chain 2, A Comparison Of The Anti-Rhinoviral Drug Binding Pocket In
Hrv14 And Hrv1a
Length = 262
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 137 FGYTLLSLSLGRRSHFVSIYRWIEKYYGKMANGCLCVTQAMQHELAQNWGIKATVLYDQP 196
FG + SLGR + V + K++ +GCL V +H+LA + G +V Y
Sbjct: 92 FGQNMFFHSLGRSGYTVHVQCNATKFH----SGCLLVVVIPEHQLASHEGGNVSVKY--- 144
Query: 197 PEFFHP 202
F HP
Sbjct: 145 -TFTHP 149
>pdb|1R08|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|1R09|2 Chain 2, Human Rhinovirus 14 Complexed With Antiviral Compound R
61837
pdb|1RMU|2 Chain 2, Three-Dimensional Structures Of Drug-Resistant Mutants Of
Human Rhinovirus 14
pdb|2R04|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2R06|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2R07|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2RM2|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2RMU|2 Chain 2, Three-Dimensional Structures Of Drug-Resistant Mutants Of
Human Rhinovirus 14
pdb|2RR1|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2RS1|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2RS3|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|2RS5|2 Chain 2, Structural Analysis Of Antiviral Agents That Interact With
The Capsid Of Human Rhinoviruses
pdb|4RHV|2 Chain 2, The Use Of Molecular-Replacement Phases For The Refinement
Of The Human Rhinovirus 14 Structure
pdb|1HRI|2 Chain 2, Structure Determination Of Antiviral Compound Sch 38057
Complexed With Human Rhinovirus 14
pdb|1HRV|2 Chain 2, Hrv14SDZ 35-682 Complex
pdb|1RUJ|2 Chain 2, Rhinovirus 14 Mutant With Ser 1 223 Replaced By Gly
(S1223g)
pdb|1RUI|2 Chain 2, Rhinovirus 14 Mutant S1223g Complexed With Antiviral
Compound Win 52084
pdb|1RUH|2 Chain 2, Rhinovirus 14 Mutant N1219s Complexed With Antiviral
Compound Win 52084
pdb|1RUG|2 Chain 2, Rhinovirus 14 Mutant N1219s Complexed With Antiviral
Compound Win 52035
pdb|1RUF|2 Chain 2, Rhinovirus 14 (Hrv14) (Mutant With Asn 1 219 Replaced By
Ala (N219a In Chain 1)
pdb|1RUE|2 Chain 2, Rhinovirus 14 Site Directed Mutant N1219a Complexed With
Antiviral Compound Win 52035
pdb|1RUD|2 Chain 2, Rhinovirus 14 Mutant N1105s Complexed With Antiviral
Compound Win 52084
pdb|1RUC|2 Chain 2, Rhinovirus 14 Mutant N1105s Complexed With Antiviral
Compound Win 52035
pdb|1VRH|2 Chain 2, Hrv14/sdz 880-061 Complex
pdb|1RVF|2 Chain 2, Fab Complexed With Intact Human Rhinovirus
pdb|1D3I|2 Chain 2, Cryo-Em Structure Of Human Rhinovirus 14 (Hrv14) Complexed
With A Two-Domain Fragment Of Its Cellular Receptor,
Intercellular Adhesion Molecule-1 (D1d2-Icam-1).
Implications For Virus-Receptor Interactions. Alpha
Carbons Only
pdb|1NA1|B Chain B, The Structure Of Hrv14 When Complexed With Pleconaril
pdb|1NCQ|B Chain B, The Structure Of Hrv14 When Complexed With Pleconaril, An
Antiviral Compound
Length = 262
Score = 32.0 bits (71), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 137 FGYTLLSLSLGRRSHFVSIYRWIEKYYGKMANGCLCVTQAMQHELAQNWGIKATVLYDQP 196
FG + SLGR + V + K++ +GCL V +H+LA + G +V Y
Sbjct: 92 FGQNMFFHSLGRSGYTVHVQCNATKFH----SGCLLVVVIPEHQLASHEGGNVSVKY--- 144
Query: 197 PEFFHP 202
F HP
Sbjct: 145 -TFTHP 149
>pdb|1RHI|2 Chain 2, Human Rhinovirus 3 Coat Protein
Length = 262
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 137 FGYTLLSLSLGRRSHFVSIYRWIEKYYGKMANGCLCVTQAMQHELAQNWGIKATVLYDQP 196
FG + SLGR + + + K++ +GCL V +H+LA + G +V Y
Sbjct: 92 FGQNMFYHSLGRTGYTIHVQCNATKFH----SGCLLVVVIPEHQLASHEGGTVSVKY--- 144
Query: 197 PEFFHP 202
++ HP
Sbjct: 145 -KYTHP 149
>pdb|1TZ0|A Chain A, Crystal Structure Of Putative Antibiotic Biosythesis
Monooxygenase From Bacillus Cereus
pdb|1TZ0|B Chain B, Crystal Structure Of Putative Antibiotic Biosythesis
Monooxygenase From Bacillus Cereus
pdb|1TZ0|C Chain C, Crystal Structure Of Putative Antibiotic Biosythesis
Monooxygenase From Bacillus Cereus
Length = 114
Score = 30.0 bits (66), Expect = 3.0, Method: Composition-based stats.
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 5/37 (13%)
Query: 426 FKGFPDDSDVLKKLRNGTLEMGLSARWATE-----WE 457
F+GF D S ++KK+R G E+ + RW +E WE
Sbjct: 37 FEGFIDLSVLVKKVRRGDEEVVVXIRWESEEAWKNWE 73
>pdb|2I71|A Chain A, Crystal Structure Of A Conserved Protein Of Unknown
Function From Sulfolobus Solfataricus P2
pdb|2I71|B Chain B, Crystal Structure Of A Conserved Protein Of Unknown
Function From Sulfolobus Solfataricus P2
Length = 400
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 377 LPMKVVDMFGCGLPVCAVSYSCIEELVKVDKNGLLFSSSSELADQLLMLFKGFPD 431
L + V D++ C A SC E +++ KN L S S +A + FKG PD
Sbjct: 70 LGISVADVYNCKY---ADYRSCKECIIQNSKNDLGISESYVVAPNVYQKFKGKPD 121
>pdb|3AXZ|A Chain A, Crystal Structure Of Haemophilus Influenzae Trmd In
Complex With Adenosine
Length = 266
Score = 28.9 bits (63), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 285 RRVAAILNEDDSTNEEVFLKEISDGKQYLYPRLLFIITGKGPDKESYEEKIRRLRLKRVA 344
R + +L + S E+ F + D Y P +L +T + E+IR+ RLK+
Sbjct: 174 RFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSL 233
Query: 345 FRTMWL 350
RT WL
Sbjct: 234 QRT-WL 238
>pdb|1UAJ|A Chain A, Crystal Structure Of Trna(M1g37)methyltransferase: Insight
Into Trna Recognition
pdb|1UAK|A Chain A, Crystal Structure Of Trna(M1g37)methyltransferase: Insight
Into Trna Recognition
pdb|1UAL|A Chain A, Crystal Structure Of Trna(M1g37)methyltransferase: Insight
Into Trna Recognition
pdb|1UAM|A Chain A, Crystal Structure Of Trna(M1g37)methyltransferase: Insight
Into Trna Recognition
Length = 274
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 285 RRVAAILNEDDSTNEEVFLKEISDGKQYLYPRLLFIITGKGPDKESYEEKIRRLRLKRVA 344
R + +L + S E+ F + D Y P +L +T + E+IR+ RLK+
Sbjct: 174 RFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSL 233
Query: 345 FRTMWL 350
RT WL
Sbjct: 234 QRT-WL 238
>pdb|2P0N|A Chain A, Nmb1532 Protein From Neisseria Meningitidis, Unknown
Function
pdb|2P0N|B Chain B, Nmb1532 Protein From Neisseria Meningitidis, Unknown
Function
Length = 172
Score = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 11/114 (9%)
Query: 168 NGCLCVTQAMQHELAQNWGIKATVLYDQPPEFFHPTSLEEKHELFCRLNKILHQPLGVQD 227
NGC + ++AQ + + A + ++ E F P L+ + ++++L Q +G+ D
Sbjct: 45 NGCNQIVLQTIRQIAQYFNVAAPLHHEDEEENFFPLLLQYAPQAQESVDELLRQHIGLHD 104
Query: 228 ---CVS---NGMEGQKA---DETIFTS-LAGIDVFLKPNRPALVVSSTSWTPDE 271
VS +E A DE F +AG DV L P L ++ P E
Sbjct: 105 NWAAVSAEFAKLEADNAYVPDEEAFKRFVAGYDVHLAIEEP-LFDXGNTFIPKE 157
>pdb|3SR7|A Chain A, Crystal Structure Of S. Mutans Isopentenyl Pyrophosphate
Isomerase
pdb|3SR7|B Chain B, Crystal Structure Of S. Mutans Isopentenyl Pyrophosphate
Isomerase
pdb|3SR7|C Chain C, Crystal Structure Of S. Mutans Isopentenyl Pyrophosphate
Isomerase
pdb|3SR7|D Chain D, Crystal Structure Of S. Mutans Isopentenyl Pyrophosphate
Isomerase
Length = 365
Score = 28.5 bits (62), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 56/124 (45%), Gaps = 17/124 (13%)
Query: 356 PLLLGSADLGVCLHTSSSGLDLPMKVVDMFGCGLPVCAVSYSCIEELVKVDKNGL----- 410
P +L G+ + T + +DL +K VD+ G G S++ IE +++ L
Sbjct: 208 PFILKEVGFGMDVKTIQTAIDLGVKTVDISGRG----GTSFAYIENRRGGNRSYLNQWGQ 263
Query: 411 ----LFSSSSELADQLLMLFK-GFPDDSDVLKKLRNGTLEMGLSARWATEWEEHAKPLIT 465
+ ++ L D++ +L G D++K L G +GLS E+H+ +
Sbjct: 264 TTAQVLLNAQPLMDKVEILASGGIRHPLDIIKALVLGAKAVGLSRTMLELVEQHS---VH 320
Query: 466 EVIS 469
EVI+
Sbjct: 321 EVIA 324
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.137 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,124,940
Number of Sequences: 62578
Number of extensions: 565192
Number of successful extensions: 1250
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1247
Number of HSP's gapped (non-prelim): 11
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)